[modeller_usage] beta-sheets and alpha-helixes

["Matthias Negri" <>]

Hello, 
my name is Matthias and I'm a PhD Student at University of Saarland. 
I'm trying to model a cypP450 with modeller7v7 by defining the secondary
structure (alpha, sheet..) in the special_restraints ROUTINE, but I
still get error messages and the job is broken up!

That's the error message I got:
"Dynamically allocated memory at         amaxseq [B,kB,MB]:     39334681
  38412.773    37.512
TOP_________>   169  174 CALL ROUTINE = 'special_restraints'

TOP_________>   170  479 SET ADD_RESTRAINTS = ON

TOP_________>   171  480 MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA',
RESIDUE_IDS = ';
                      228:A' '253:A'

assgn___215E> Dynamic memory allocation failed.
              Routine, variable, status:  vars%val         1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1"

While my top file (special_restraints) is:
"SUBROUTINE ROUTINE = 'special_restraints'
 
  SET ADD_RESTRAINTS = on
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '228:A' '253:A'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '140:A' '159:A'
  MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '464:A' '467:A'
  MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '480:A' '484:A'
  MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '490:A' '495:A'

  RETURN
END_SUBROUTINE"

1.Can you tell me what the reason for failing is?
2.Further, does modeller8.1 resolve this problem (if there is a bug in
mod7v7?)!
3.I even get the error disclaimer:
"openf5__224_> Open       11  OLD  SEQUENTIAL 
${MODINSTALL7v7}/modlib/sched.lib
TOP_________>   196  233 WRITE_SCHEDULE FILE = SCHFILE

openf5__224_> Open       14  UNKNOWN  SEQUENTIAL  CYP17.sch
TOP_________>   197  234 DO  IREPEAT = 1  REPEAT_OPTIMIZATION  1

TOP_________>   198  235 CALL ROUTINE = 'single_model_pass'

TOP_________>   199  253 READ_MODEL FILE = MODEL,MODEL_SEGMENT = '31:A'
'496:A'

openf5__224_> Open       11  OLD  SEQUENTIAL  Mixed1.ini
openf5__224_> Open       11  OLD  SEQUENTIAL  Mixed1.ini
rdatm___297_> Segments, residues, atoms:        1      466     7457
rdatm___298_> Segment:        1    31 A   496 A     7457
TOP_________>   200  254 DO SCHEDULE_STEP = 1  N_SCHEDULE  1

TOP_________>   201  255 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM',
RESULT = ID;
                      1

TOP_________>   202  256 PICK_RESTRAINTS ADD_RESTRAINTS = OFF

nselat__596E> Atom index is out of range (iatm,natm):     7458     7457
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:     39111561   "
What's the reason for, where I do mistakes?

Thanks in advance, 
 
Matthias Negri 
 
8.2 Pharmaceutical and  Medicinal Chemistry 
 Saarland University 
 P.O.Box 151150  
 66041 Saarbrücken, Germany 
 phone: 	+49-681-302-2980 
 fax:		+49-681-302-4386  
 Email: 	 
 http://www.uni-saarland.de/fak8/hartmann 
 
Computational Medicinal Chemistry Group 
Dept. of Pharmaceutical Sciences, University of Bologna 
Via Belmeloro, 6;   40100 Bologna, Italy 
Email: 		 
http://www.scfarm.unibo.it